BackgroundSince 1990, the lives of 48 million children under the age of 5 years have been saved because of increased investments in reducing child mortality. However, despite these unprecedented gains, 250 million children younger than 5 years in low- and middle-income countries (LMIC) cannot meet their developmental potential due to poverty, poor health and nutrition, and lack of necessary stimulation and care. Lesotho has high levels of poverty, HIV, and malnutrition, all of which affect child development outcomes. There is a unique opportunity to address these complex issues through the widespread network of informal preschools in rural villages in the country, which provide a setting for inclusive, integrated Early Childhood Care and Development (ECCD) and HIV and nutrition interventions.MethodsWe are conducting a cluster randomised controlled trial in Mokhotlong district, Lesotho, to evaluate a newly developed community-based intervention program to integrate HIV-testing and treatment services, ECCD, and nutrition education for caregivers with children aged 1–5 years living in rural villages. Caregivers and their children are randomly assigned by village to intervention or control condition. We select, train, and supervise community health workers recruited to implement the intervention, which consists of nine group-based sessions with caregivers and children over 12 weeks (eight weekly sessions, and a ninth top-up session 1 month later), followed by a locally hosted community health outreach day event. Group-based sessions focus on using early dialogic book-sharing to promote cognitive development and caregiver-child interaction, health-related messages, including motivation for HIV-testing and treatment uptake for young children, and locally appropriate nutrition education. All children aged 1–5 years and their primary caregivers living in study villages are eligible for participation. Caregivers and their children will be interviewed and assessed at baseline, after completion of the intervention, and 12 months post intervention.DiscussionThis study provides a unique opportunity to assess the potential of an integrated early childhood development intervention to prevent or mitigate developmental delays in children living in a context of extreme poverty and high HIV rates in rural Lesotho. This paper presents the intervention content and research protocol for the study.Trial registrationThe Mphatlalatsane: Early Morning Star trial is registered on the International Standard Randomized Controlled Trial Number database, registration number ISRCTN16654287; the trial was registered on 3 July 2015.